Although the global health emergency posed by the Zika virus (ZIKV) outbreak associated with severe neonatal neurological conditions has subsided, the continued transmission of ZIKV in endemic regions remains. As such, there is maintained interest in elucidating and developing interventions against ZIKV, a arthropod-borne flavivirus. To identify small-molecule anti-Zika compounds, we screened a collection of 6,000 compounds, most derived from natural products, for their ability to block wild-type ZIKV infection. We used a viral cytopathic effect (CPE) inhibition assay conducted in Vero cells that was optimized and miniaturized to 1536-well format. Suitably active compounds identified from the primary assay were subjected to a panel of orthogonal assays using recombinant Zika viruses, one using a recombinant Renilla luciferase reporter assay, the other a novel mCherry reporter system. Six active molecules were further evaluated for their inhibitory effects against other flaviviruses. Lastly, we developed a novel viral pathogenicity model in a 3D-bioprinted retinal tissue to better replicate in vivo infections of targeted Zika tissues in humans.